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Matthew Blakeley

►  Instrument and research scientist responsible for the macromolecular crystallography beamlines LADI-III and DALI

Main areas of expertise : Structural Biology, neutron macromolecular crystallography, neutron instrumentation

E-mail

blakeleym(at)ill.fr
LocationScience Building (3rd floor), office 316

Phone

Phone : +33 (0)4 76 20 70 54

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Instrument and research scientist in the Large-Scale Structures group at ILL.

Responsible for the neutron quasi-Laue diffractometers LADI-III and DALI

The quasi-Laue diffractometer LADI-III (since 1995 as LADI and 2007 as LADI-III) is used for single crystal neutron studies at high resolution (2.5 – 1.5 Å) of biological macromolecules, such as proteins or nucleic acids, providing unique information that is complementary to X-ray crystallography. Locating the positions of hydrogen/deuterium (H/D) atoms and protons/deuterons (H+/D+) in a macromolecule, provides us with knowledge of the protonation states of key amino-acid residues, ligands or inhibitors, and the orientation of bound water molecules. These details allow a more complete understanding of a macromolecule’s specific function and behaviour.

Due to the low flux of even the most intense neutron sources, neutron macromolecular crystallography has historically been an intensity limited technique, requiring very large crystal volumes and long acquisition times. However, over the years, LADI-III has gone through a number of upgrades that have dramatically reduced both the crystal volumes required and the data collection times. This has placed LADI-III's performance in a world-leading position, despite the more recent appearance of instruments at other neutron facilities, such as BioDiff at FRM-II, MaNDi at SNS and iBIX at J-Parc. The smallest crystals used, largest systems studied and fastest data collections have all been achieved using LADI-III. Currently, LADI-III utilizes a multilayer bandpass filter for wavelength selection. The replacement of the multilayer bandpass filter with a neutron velocity selector is a planned future upgrade for LADI-III that will increase the neutron transmission by a factor of 2-3 and will allow more flexibility (in terms of wavelength bandwidth choice) so as to further optimize data collection strategies.

To extend the capabilities and capacity for neutron macromolecular crystallography experiments at ILL, a second quasi-Laue diffractometer DALI has been commissioned at H141 as part of the ILL Endurance Programme. DALI utilizes a neutron velocity selector to provide both higher transmission and a narrower bandwidth (δλ/λ ~10%) than LADI-III, required to extend capabilities to studies of larger, more complex systems.

In October 2025, a completely new neutron-sensitive cylindrical image plate detector was built and installed on DALI and neutron diffraction tests and analyses were performed using crystals of proteins covering a wide range of molecular weights, from the very small (6 kDa) to the very large (271 kDa). The results show that the LADI-III and DALI neutron protein crystallography diffractometers are highly complementary; LADI-III delivers higher quality diffraction data for small to medium-sized proteins (5-70 kDa) and DALI, with its new detector and narrow bandwidth velocity selector, now delivers diffraction data of higher quality for large proteins (70-150 kDa). In addition, the tests indicate that DALI can even be used to study very large proteins (>150 kDa) that were previously out of range. This represents a step change in capabilities for neutron protein crystallography research and further cements the ILL’s position as world-leading in the field.

LADI-III and DALI are dedicated to high-resolution (dmin ~1.5-2.5 Å) neutron crystallographic studies of biomacromolecules (proteins, oligonucleotides etc.,) and their complexes, in order to locate hydrogen/deuterium (H/D) atoms and protons/deuterons (H+/D+) of special interest, thereby revealing important information on protonation, H-bonding and hydration.

Neutron macromolecular crystallography is unique in its ability to provide these invaluable details at room-temperature, and without radiation damage issues, which can be critical for understanding enzyme catalysis or ligand-binding, and can be used to help guide structure-based drug design.

Some highlight examples are given below...

  1. Neutron diffraction reveals protonation states in pyridoxal-5'-phosphate-free and glycine external aldimine-bound serine hydroxymethyltransferase. Drago et al., FEBS J. (2025) online ahead of print.
  2. Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase. Drago et al., Cell Rep. Phys. Sci. (2024) 5(2):101827.
  3. Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease. Kneller et al., Nat. Commun. (2022) 13(1), 2268.
  4. Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding. Gajdos et al., Nat. Commun. (2022) 13(1), 194.
  5. Visualizing the protons in a metalloenzyme electron proton transfer pathway. Kwon et al., Proc. Natl. Acad. Sci. U.S.A. (2020) 117(12), 6484-6490.
  6. Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. Halsted et al., IUCrJ (2019) 6(4), 761-772.
  7. Zooming in on protons: Neutron structure of protein kinase A trapped in a product complex. Gerlits et al., Sci. Adv. (2019) 5(3), eaav0482.
  8. A molecular mechanism for transthyretin amyloidogenesis. Yee et al., Nat. Commun. (2019) 10, 925.
  9. Elucidation of hydrogen bonding patterns in ligand-free, lactose- and glycerol-bound galectin-3C by neutron crystallography to guide drug design. Manzoni et al., J. Med. Chem. (2018) 61(10), 4412-4420.
  10. "To be or not to be" protonated: Atomic details of human carbonic anhydrase-clinical drug complexes by neutron crystallography and simulation. Kovalevsky et al., Structure (2018) 26(3), 383-390.
  11. Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme. Dajnowicz et al., Nat. Commun. (2017) 8, 955.
  12. Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100K. Gerlits et al., J. Med. Chem. (2017) 60(5), 2018–2025.
  13. Direct visualization of a Fe(IV)–OH intermediate in a heme enzyme. Kwon et al., Nat. Commun. (2016) 7, 13445.
  14. Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site. Gerlits et al., Angew. Chem. Int. Ed. Engl. (2016)55(16), 4924-4927.
  15. Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase. Casadei et al., Science (2014) 345(6193), 193-197.  The following commentary article was also written for this work; Biochemistry. Fishing for peroxidase protons. Groves & Boaz Science (2014) 345(6193), 142-143.
  16. Joint X-ray/neutron crystallographic study of HIV-1 protease with clinical inhibitor amprenavir - insights for drug design. Weber et al., J. Med. Chem. (2013) 56(13), 5631–5635.

IRGA PhD project.

3-year PhD research project (Théodore Arnaud) focused on using neutron crystallography to unravel how pathogens interact with human glycolipids. This is a collaborative PhD project between the ILL and CERMAV at the Université Grenoble Alpes, as part of the GATES project.

EU AMBER co-fund. 

3-year postdoctoral research project (Currently unfilled) focused on visualizing key hydrogen atoms in carbohydrate-binding proteins and their complexes. Part of the EU AMBER co-fund and coordinated by LINXS.

ILL (LSS/CS) Esmeralda project. 

3-year postdoctoral project (Dr. Santiago Alonso Gil) between the Computing for Science and LSS groups at the ILL. The project is focused on the expansion and further development of the ILL’s Laue data reduction software, initially developed by Juan Rodriguez-Carvajal et al.

Full list:

  1. Neutron diffraction reveals protonation states in pyridoxal-5'-phosphate-free and glycine external aldimine-bound serine hydroxymethyltransferase. Drago et al., FEBS J. (2025) online ahead of print.
  2. Current and future perspectives for structural biology at the Grenoble EPN campus: a comprehensive overview. McCarthy et al., J Synchrotron Radiat. (2025) 32(3):1-18.
  3. Counter-diffusion studies of human transthyretin: the growth of high-quality crystals for X-ray and neutron crystallography. De'Ath et al., J Appl. Crystallogr. (2025) 58(1):107-118.
  4. Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase. Drago et al.,Cell Rep. Phys. Sci. (2024) 5(2):101827.
  5. Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase. Sørensen et al.,ACS Omega (2023) 8(32):29101-29112.
  6. Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography. Drago et al.,Commun. Chem. (2023) 6(1):162.
  7. An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction. Drago et al., Chem. Sci. (2022) 13(34), 10057-10065.
  8. Microgravity crystallization of perdeuterated tryptophan synthase for neutron diffraction. Drago et al., NPJ Microgravity. (2022) 8(1), 13.
  9. Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease. Kneller et al., Nat. Commun. (2022) 13(1), 2268.
  10. Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding. Gajdos et al., Nat. Commun. (2022) 13(1), 194.
  11. Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps. Kelpšas et al., IUCrJ. (2021) 8(4), 633-643.
  12. Human myelin protein P2: from crystallography to time-lapse membrane imaging and neuropathy-associated variants. Uusitalo et al., FEBS J. (2021) 288(23), 6716-6735.
  13. Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure. Gerlits et al., Curr. Res. Struct. Biol. (2021) 3, 206-215.
  14. Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions. Gajdos et al.,Structure (2021) 29(9), 1003-1013. The following commentary article was written for this work; In structural glycobiology, Deuterium provides the details. Vasta & Amzel Structure (2021) 29(9), 937-939.
  15. Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis. McGregor et al.,IUCrJ (2021) 8(1), 46-59.
  16. Production of perdeuterated fucose from glyco-engineered bacteria. Gajdos et al.,Glycobiology (2021) 31(2), 151-158.
  17. Visualizing tetrahedral oxyanion bound in HIV-1 protease using neutrons: Implications for the catalytic mechanism and drug design. Kumar et al.,ACS Omega (2020) 5(20), 11605-11617.
  18. Visualizing the protons in a metalloenzyme electron proton transfer pathway. Kwon et al.,Proc. Natl. Acad. Sci. U.S.A. (2020) 117(12), 6484-6490.
  19. Heme peroxidase - Trapping intermediates by cryo neutron crystallography. Kwon et al.,Methods Enzymol. (2020) 634, 379-389.
  20. Protein kinase A in the neutron beam: Insights for catalysis from directly observing protons. Gerlits et al.,Methods Enzymol. (2020) 634, 311-331.
  21. Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease. Kovalevsky et al.,Methods Enzymol. (2020) 634, 257-279.
  22. Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. Halsted et al.,IUCrJ (2019) 6(4), 761-772.
  23. Perdeuteration, large crystal growth and neutron data collection of Leishmania mexicana triose-phosphate isomerase E65Q variant. Kelpšas et al.,Acta Cryst.F (2019) 75(4), 1-10.
  24. Zooming in on protons: Neutron structure of protein kinase A trapped in a product complex. Gerlits et al.,Sci. Adv. (2019) 5(3), eaav0482.
  25. A molecular mechanism for transthyretin amyloidogenesis. Yee et al.,Nat. Commun. (2019) 10, 925.
  26. Using neutron crystallography to elucidate the basis of selective inhibition of carbonic anhydrase by saccharin and a derivative. Koruza et al.,J. Struct. Biol. (2019) 205, 147–154.
  27. Temperature-induced replacement of phosphate proton with metal ion captured in neutron structures of A-DNA. Vandavasi et al.,Structure (2018) 26, 1645–1650.
  28. Elucidation of hydrogen bonding patterns in ligand-free, lactose- and glycerol-bound galectin-3C by neutron crystallography to guide drug design. Manzoni et al.,J. Med. Chem. (2018) 61(10), 4412-4420.
  29. Neutron crystallography detects differences in protein dynamics: Structure of PKG II cyclic nucleotide binding domain in complex with an activator. Gerlits et al.,Biochemistry (2018) 57(12), 1833-1837.
  30. Neutron macromolecular crystallography. Blakeley & Podjarny Emerg. Top. Life Sci. (2018) 2(1), 39-55.
  31. "To be or not to be" protonated: Atomic details of human carbonic anhydrase-clinical drug complexes by neutron crystallography and simulation.Kovalevsky et al.,Structure (2018) 26(3), 383-390.
  32. Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme. Dajnowicz et al.,Nat. Commun. (2017) 8, 955.
  33. Back-exchange of deuterium in neutron crystallography: characterization by IR spectroscopy. Yee et al.,J. Appl. Cryst. (2017) 50, 660-664.
  34. Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100K. Gerlits et al.,J. Med. Chem. (2017) 60(5), 2018–2025.
  35. An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase. Golden et al.,Sci. Rep. (2017) 7, 40517.
  36. Direct visualization of a Fe(IV)–OH intermediate in a heme enzyme. Kwon et al.,Nat. Commun. (2016) 7, 13445.
  37. Perdeuteration, crystallization, data collection and comparison of five neutron diffraction data sets of complexes of human galectin-3C. Manzoni et al.,Acta Cryst. D (2016) 72(11), 1194-1202.
  38. Neutron crystallography aids in drug design. Blakeley IUCrJ (2016) 3(5), 296-297.
  39. Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site. Gerlits et al.,Angew. Chem. Int. Ed. Engl. (2016)55(16), 4924-4927.
  40. High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP–oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution. Howard et al.,IUCrJ (2016) 3(2), 1-12.
  41. Production, crystallization and neutron diffraction of fully deuterated human myelin peripheral membrane protein P2. Laulumaa et al.,Acta Cryst. F (2015) 71(11), 1391-1395.
  42. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential. Blakeley et al.,IUCrJ (2015) 2(4), 464-474.
  43. Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography. Fisher et al.,Acta Cryst. D (2014) 70(12), 3266-3272.
  44. Neutron diffraction reveals hydrogen bonds critical for cGMP-selective activation: Insights for cGMP-dependent protein kinase agonist design. Huang et al.,Biochemistry (2014) 53(43), 6725–6727.
  45. Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein. Haupt et al.,IUCrJ (2014) 1(6), 429-438.
  46. L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study. Langan et al.,Structure (2014) 22(9), 1287-1300.
  47. Neutron cryo-crystallography captures the protonation state of ferryl heme in a peroxidase. Casadei et al.,Science (2014) 345(6193), 193-197.The following commentary article was also written for this work; Biochemistry. Fishing for peroxidase protons. Groves & Boaz Science (2014) 345(6193), 142-143.
  48. The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation. Oksanen et al.,PLoS ONE (2014) 9(1), e86651.
  49. Joint X-ray/neutron crystallographic study of HIV-1 protease with clinical inhibitor amprenavir - insights for drug design. Weber et al.,J. Med. Chem. (2013) 56(13), 5631–5635.
  50. Near-atomic resolution neutron crystallography on perdeuterated Pyrococcus furiosus rubredoxin: Implication of hydronium ions and protonation state equilibria in redox changes. Cuypers et al.,Angew. Chem. Int. Ed. Engl. (2012)52(3), 1022-1025.
  51. Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction. Hughes et al.,Acta Cryst. F (2012)68(12), 1482-1487.
  52. Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography. Kovalevsky et al.,Acta Cryst. D (2012)68(9), 1201-1206.
  53. Neutron protein crystallography at ultra-low (<15K) temperatures. Myles et al.,J. Appl. Cryst. (2012)45(4), 686-692.
  54. Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness. Fisher et al.,Acta Cryst. D (2012)68(7), 800-809.
  55. Rapid visualization of hydrogen positions in protein neutron crystallographic structures. Munshi et al.,Acta Cryst. D (2012)68(1), 35-41.
  56. Preliminary neutron crystallographic study of human transthyretin. Haupt et al.,Acta Cryst. F (2011) 67(11), 1428-1431.
  57. Neutron structure of type-III Antifreeze Protein allows the reconstruction of AFP-ice interface. Howard et al.,J. Molec. Recognit. (2011) 24(4), 724-732.
  58. The active site protonation states of perdeuterated Toho-1 β-lactamase determined by neutron diffraction support a role for Glu166 as the general base in acylation. Tomanicek et al.,FEBS Lett. (2011) 585, 364-368.
  59. Identification of the elusive hydronium ion exchanging roles with a proton in an enzyme at lower pH values. Kovalevsky et al.,Angew. Chem. Int. Ed. Engl. (2011) 50(33), 7520-7523. The following commentary article was written for this work; Ion-protein coordination: the many faces of a proton. Davidson VL. Nat. Chem. (2011) 3(9), 662-663.
  60. Neutron macromolecular crystallography with LADI-III. Blakeley et al.,Acta Cryst. D (2010) 66(11), 1198-1205.
  61. Combined neutron and X-ray diffraction studies of DNA in crystals and solutions. Leal et al.,Acta Cryst. D (2010) 66(11), 1244-1248.
  62. Sweet neutron crystallography. Teixeira et al.,Acta Cryst.D (2010) 66(11), 1139-1143.
  63. Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint X-ray and neutron diffraction study. Kovalevsky et al.,Structure (2010) 18(6), 688-699.  The following commentary article was written for this work; The lighter side of a sweet reaction. Bennett & Yeager Structure (2010) 18(6), 657-659.
  64. Incorporation of methyl-protonated valine and leucine residues into deuterated ocean pout type III antifreeze protein: expression, crystallization and preliminary neutron diffraction studies. Petit-Haertlein et al.,Acta Cryst.F (2010) 66(6), 665-669.
  65. Unambiguous determination of hydrogen atom positions: comparing results from neutron and high-resolution X-ray crystallography. Gardberg et al.,Acta Cryst. D (2010) 66, 558-567.
  66. Neutron diffraction studies of a class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant. Tomanicek et al.,J. Mol. Biol. (2010) 396(4), 1070-1080.
  67. Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase. Oksanen et al.,J. R. Soc. Interface (2009) 6(5), S599-610.
  68. Characterization of image plates for neutron diffraction. Wilkinson et al.,J. Appl. Cryst. (2009) 42, 749-757.
  69. Perdeuteration, purification, crystallization and preliminary neutron diffraction of an ocean pout type III antifreeze protein. Petit-Haertlein et al.,Acta Cryst. F (2009) 65(4), 406-409.
  70. A preliminary neutron crystallographic study of an A-DNA crystal. Leal et al.,Acta Cryst. F (2009) 65(3), 232-235.
  71. A preliminary neutron diffraction study of gamma-chymotrypsin. Novak et al.,Acta Cryst. F (2009) 65(3), 317-320.
  72. A preliminary neutron crystallographic study of proteinase K at pD 6.5. Gardberg et al.,Acta Cryst. F (2009) 65(2), 184-187.
  73. Neutron macromolecular crystallography. Blakeley Cryst. Rev. (2009) 15(3), 157-218.
  74. Neutron crystallography: opportunities, challenges, and limitations. Blakeley et al.,Curr. Opin. Struct. Biol. (2008) 18(5), 593-600.
  75. Preliminary neutron crystallographic analysis of selectively CH3-protonated deuterated rubredoxin from Pyrococcus furiosus. Weiss et al.,Acta Cryst. F (2008) 64(6), 537-540.
  76. A preliminary neutron crystallographic study of thaumatin. Teixeira et al.,Acta Cryst. F (2008) 64(5), 378-381.
  77. New sources and instrumentation for neutrons in biology. Teixeira et al.,Chem. Phys. (2008) 345(2-3), 133-151.
  78. Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase. Blakeley et al.,Proc. Natl. Acad. Sci. U.S.A. (2008) 105(6), 1844-1848.
  79. The determination of protonation states in proteins. Ahmed et al.,Acta Cryst. D (2007) 63(8), 906-922.
  80. Comparison of hydrogen determination with X-ray and neutron crystallography in a human aldose reductase-inhibitor complex. Blakeley et al.,Eur. Biophys. J. (2006) 35(7), 577-583.
  81. Neutron Laue macromolecular crystallography. Meilleur et al.,Eur. Biophys. J. (2006) 35(7), 611-620.
  82. A preliminary neutron diffraction study of rasburicase, a recombinant urate oxidase enzyme, complexed with 8-azaxanthin. Budayova-Spano et al.,Acta Cryst. F (2006) 62(3), 306-309.
  83. High-resolution neutron protein crystallography with radically small crystal volumes: application of perdeuteration to human aldose reductase. Hazemann et al.,Acta Cryst. D (2005) 61(10), 1413-1417.
  84. The 15-K neutron structure of saccharide-free concanavalin A. Blakeley et al.,Proc. Natl. Acad. Sci. U.S.A. (2004) 101(47), 16405-16410. The following commentary articles were written for this work; (i) Getting protein solvent structures down cold. Hanson Proc. Natl. Acad. Sci. U.S.A. (2004) 101(47), 16393-16394.  (ii) Some like it (very) cold. Finkelstein Nature (2004) 432, 288.
  85. Synchrotron and neutron techniques in biological crystallography. Blakeley et al.,Chem. Soc. Rev. (2004) 33(8), 548-557.